Mime Kobayashi

Fabrication of Aligned Magnetic Nanoparticles Using Tobamoviruses

We used genetically modified tube-shaped tobamoviruses to produce 3 nm aligned magnetic nanoparticles. Amino acid residues facing the central channel of the virus were modified to increase the number of nucleation sites. Energy dispersive X-ray spectroscopy and superconducting quantum interference device analysis suggest that the particles consisted of Co-Pt alloy. The use of tobamovirus mutants is a promising approach to making a variety of components that can be applied to fabricate nanometer-scaled electronic devices.

A self-assembled protein nanotube with high aspect ratio.

Production of a self-assembled protein nanotube achieved through engineering of the 11mer ring protein trp RNA-binding attenuation protein is described. The produced mutant protein is able to stack in solution to produce an extremely narrow, uniform nanotube apparently stabilized by a mixture of disulfide bonds and hydrophobic interactions. Assembly is reversible and the length of tube can potentially be controlled. Large quantities of hollow tubes 8.5 nm in overall diameter with lengths varying from 7 nm to over 1 microm are produced. The structure is analyzed using transmission electron microscopy, atomic force microscopy, mass spectrometry, and single-particle analysis and it is found that component rings stack in a head-to-head fashion. The internal diameter of the tube is 2.5 nm, and the amino acid residues lining the central cavity can be mutated, raising the possibility that the tube can be filled with a variety of conducting or semiconducting materials.

Janus-like Protein Cages. Spatially Controlled Dual-Functional Surface Modifications of Protein Cages

Protein cages have been used both as size-constrained reaction vessels for nanomaterials synthesis and as nanoscale building blocks for higher order nanostructures. We generated Janus-like protein cages, which are dual functionalized with a fluorescent and an affinity label, and demonstrated control over both the stoichiometry and spatial distribution of the functional groups. The capability to toposelectively functionalize protein cages has allowed us to manipulate hierarchical assembly using the layer-by-layer assembly process. Janus-like protein cages expand the toolkit of nanoplatforms that can be used for directed assembly of nanostructured materials.

Conservation of functional domain structure in bicarbonate-regulated "soluble" adenylyl cyclases in bacteria and eukaryotes.

Soluble adenylyl cyclase (sAC) is an evolutionarily conserved bicarbonate sensor. In mammals, it is responsible for bicarbonate-induced, cAMP-dependent processes in sperm required for fertilization and postulated to be involved in other bicarbonate- and carbon dioxide-dependent functions throughout the body. Among eukaryotes, sAC-like cyclases have been detected in mammals and in the fungi Dictyostelium; these enzymes display extensive similarity extending through two cyclase catalytic domains and a long carboxy terminal extension. sAC-like cyclases are also found in a number of bacterial phyla (Cyanobacteria, Actinobacteria, and Proteobacteria), but these enzymes generally possess only a single catalytic domain and little, if any, homology with the remainder of the mammalian protein. Database mining through a number of recently sequenced genomes identified sAC orthologues in additional metazoan phyla (Arthropoda and Chordata) and additional bacterial phyla (Chloroflexi). Interestingly, the Chloroflexi sAC-like cyclases, a family of three enzymes from the thermophilic eubacterium, Chloroflexus aurantiacus, are more similar to eukaryotic sAC-like cyclases (i.e., mammalian sAC and Dictyostelium SgcA) than they are to other bacterial adenylyl cyclases (ACs) (i.e., from Cyanobacteria). The Chloroflexus sAC-like cyclases each possess two cyclase catalytic domains and extensive similarity with mammalian enzymes through their carboxy termini. We cloned one of the Chloroflexus sAC-like cyclases and confirmed it to be stimulated by bicarbonate. These data extend the family of organisms possessing bicarbonate-responsive ACs to numerous phyla within the bacterial and eukaryotic kingdoms.

Site-directed delivery of ferritin-encapsulated gold nanoparticles

Newly designed porter proteins, which catch gold nanoparticles and deliver the nanoparticles selectively to a silicon dioxide (SiO(2)) surface under the specific conditions were reported. Recombinant apoferritin subunits, each of which has gold-binding peptide and titanium-binding peptide at the C- and N-terminus, respectively, can efficiently encapsulate a gold nanoparticle. The bio-conjugate, a nanogold and surrounding mutant protein subunits, had a property which can deliver itself to the SiO(2) surface through the interaction. In theory, our genetically manipulated apoferritin subunits can encapsulate gold nanoparticles of various sizes, which is a promising property for applications involving surface plasmon resonance.

A helical lid converts a sulfotransferase to a dehydratase

We report here the crystal structure of retinol dehydratase, an enzyme that catalyzes the synthesis of anhydroretinol. The enzyme is a member of the sulfotransferase superfamily and its crystal structure reveals the insertion of a helical lid into a canonical sulfotransferase fold. Site-directed mutations demonstrate that this inserted lid is necessary for anhydroretinol production but not for sulfonation; thus, insertion of a helical lid can convert a sulfotransferase into a dehydratase.

Cell-type-specific regulation of the retinoic acid receptor mediated by the orphan nuclear receptor TLX.

ABSTRACT Malformations in the eye can be caused by either an excess or deficiency of retinoids. An early target gene of the retinoid metabolite, retinoic acid (RA), is that encoding one of its own receptors, the retinoic acid receptor β (RARβ). To better understand the mechanisms underlying this autologous regulation, we characterized the chick RARβ2 promoter. The region surrounding the transcription start site of the avian RARβ2 promoter is over 90% conserved with the corresponding region in mammals and confers strong RA-dependent transactivation in primary cultured embryonic retina cells. This response is selective for RAR but not retinoid X receptor-specific agonists, demonstrating a principal role for RAR(s) in retina cells. Retina cells exhibit a far higher sensitivity to RA than do fibroblasts or osteoblasts, a property we found likely due to expression of the orphan nuclear receptor TLX. Ectopic expression of TLX in fibroblasts resulted in increased sensitivity to RA induction, an effect that is conserved between chick and mammals. We have identified a cis element, the silencing element relieved by TLX (SET), within the RARβ2 promoter region which confers TLX- and RA-dependent transactivation. These results indicate an important role for TLX in autologous regulation of the RARβ gene in the eye.

A water-soluble carbon nanotube network conjugated by nanoparticles with defined nanometre gaps

Cage-shaped proteins with an affinity for carbonaceous materials were constructed and used to assemble a nanostructure in which single-walled carbon nanotubes are surrounded by cobalt oxide nanoparticles with nanometre gaps. By changing the size of proteins and materials incorporated inside the cavity, similar structures with distinctively different properties can be fabricated.

Chiral meta-molecules consisting of gold nanoparticles and genetically engineered tobacco mosaic virus

We demonstrate a chiral meta-molecule in the ultraviolet (UV) and visible (VIS) regions using a complex of Au nanoparticles (NPs) and rod-shaped tobacco mosaic virus (TMV). Au NPs five nm in diameter are uniformly formed on peptide-modified TMV. The peptide-modified TMV with uniform-sized Au NPs has improved dispersion in solution. A negative circular dichroism (CD) peak is produced around 540 nm, at plasmonic resonance wavelength of Au NPs. Additionally, modification of a CD peak in the UV region is observed. Attaching NPs to a virus causes the enhancement and modification of CD peaks in both the UV and VIS regions. Our results open a new avenue for the preparation of three dimensional chiral metamaterials at optical frequencies.

Adsorption Properties of a Gold-Binding Peptide Assessed by its Attachment to a Recombinant Apoferritin Molecule

The adsorption properties of a recombinant apoferritin protein fused to a gold-binding peptide were characterized. The results of quartz crystal microbalance measurements showed that the fusion protein preferentially adsorbs to gold surfaces. Scanning electron microscopy also revealed that the protein selectively adsorbed onto a nanometer-scale gold pattern on a SiO2 surface fabricated by electron-beam lithography. Our results indicate that nanodots and nanowires synthesized using a biotemplate can be selectively placed onto a gold surface by genetically modifying the outer surface of the biotemplate. This technique represents an important step toward biotemplate-mediated fabrication of a nanometer-scaled device that utilizes gold electrodes.